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WO2002008469A9 - Procedes, systemes et articles manufactures destines a evaluer des donnees biologiques - Google Patents

Procedes, systemes et articles manufactures destines a evaluer des donnees biologiques

Info

Publication number
WO2002008469A9
WO2002008469A9 PCT/US2001/023629 US0123629W WO0208469A9 WO 2002008469 A9 WO2002008469 A9 WO 2002008469A9 US 0123629 W US0123629 W US 0123629W WO 0208469 A9 WO0208469 A9 WO 0208469A9
Authority
WO
WIPO (PCT)
Prior art keywords
algorithm
allele
ofthe
quality value
data
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Ceased
Application number
PCT/US2001/023629
Other languages
English (en)
Other versions
WO2002008469A3 (fr
WO2002008469A2 (fr
Inventor
Heinz Breu
Hugh J Pasika
Yuandan Lou
David P Holden
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Applied Biosystems Inc
Original Assignee
Applera Corp
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Applera Corp filed Critical Applera Corp
Priority to JP2002513951A priority Critical patent/JP2004516455A/ja
Priority to AU2002211212A priority patent/AU2002211212A1/en
Priority to EP01979226A priority patent/EP1349960A2/fr
Priority to CA002416764A priority patent/CA2416764A1/fr
Publication of WO2002008469A2 publication Critical patent/WO2002008469A2/fr
Anticipated expiration legal-status Critical
Publication of WO2002008469A3 publication Critical patent/WO2002008469A3/fr
Publication of WO2002008469A9 publication Critical patent/WO2002008469A9/fr
Ceased legal-status Critical Current

Links

Classifications

    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids

Definitions

  • This invention relates to data methods and systems for assigning values to nucleic information.
  • the methods and systems are used for assigning values to nucleic information.
  • variations between individuals may signify predisposition to a disease or other
  • amplified material By determining the fragment length, one can determine the number of
  • Figure 4 depicts a flow chart ofthe steps performed by the committee machine of Figure 1 for use with methods and systems consistent with certain embodiments ofthe present invention.
  • the parameter k is called the "Baseline Window Size”. Similarly, the baselining component
  • the positive structure can be eliminated by executing
  • nucleotide lengths 110, 114, 117, 120, and 125 may be used.
  • primer peak locates within the first half of the signal and the size standard fragments locate in the
  • An in-lane size standard is a set of peaks resulting from running a size standard on an
  • H [2722, 6219, 1060, 5380, 7726, 1082, 7424, 1263, 7335, 7937, 1562].
  • edges (i,j) and (j,k) define a ratio r ⁇ . of lengths:
  • the global methods determine the size/f ⁇ of a fragment at scan number J: by evaluating a function/! The function depends on the method:
  • a scan number x corresponds to time (since the capillary length, or well-to-read distance, is fixed), and so is inversely proportional to mobility.
  • certain embodiments ofthe Envelope Caller may include the following:
  • the heuristic caller assumes that there are a maximum of two
  • committee machine 110 If there is no call for the Heuristic algorithm, and the same call for the Envelope method and the Optimizer, committee machine 110 passes those calls to the user and assigns a confidence value of 0.621. If only the Optimizer produces a call, committee machine 110 assigns a confidence value of 0.692 correct. And finally, any cases that do not fit into the above scenarios are assigned the calls given by the Heuristic algorithm and are assigned a confidence value of 0.771.
  • the above listed determination of agreement is exemplary. One skilled in the art will appreciate that other determinations of confidences are available. For example, additional algorithms may be used to produce more accurate confidence levels according to certain embodiments.
  • preprocessing simply involves sampling the original signal to reduce its dimensionality. This can be performed by calculating the most important features of the signal; the peaks and valleys. By representing the signal in such a compact form, the search space is reduced significantly.
  • the peaks form the set of candidate allele peaks that will be considered as possibilities for the allele calls.
  • the next two boxes show the varying the parameters and the calculation ofthe residual. This process is iterated, and in the final box, a winning set of allele peaks (it could be a set of one peak) is declared. Actual output ofthe algorithm is contained in Figure 15.
  • the call is made by finding the maximums in each of panels 1 and 2.
  • the individual algorithms may not be optimal when employed alone.
  • CTR cathode
  • LCD liquid crystal display
  • This input device typically has two degrees of freedom in two axes, a first axis (e.g., x) and a second axis (e.g., y), that allows the device to specify positions in a plane.

Landscapes

  • Physics & Mathematics (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • Biophysics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Chemical & Material Sciences (AREA)
  • Analytical Chemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Management, Administration, Business Operations System, And Electronic Commerce (AREA)
  • Measurement Of The Respiration, Hearing Ability, Form, And Blood Characteristics Of Living Organisms (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
  • Complex Calculations (AREA)

Abstract

L'invention concerne des procédés, systèmes et articles manufacturés destinés à réaliser des appels d'allèles. Dans certains modes de réalisation, l'appel d'allèles est effectué par une machine commune recevant des appels provenant d'une pluralité d'algorithmes d'appel d'allèles. Ladite machine commune effectue des appels présentant un degré de confiance élevé à différents niveaux. Dans d'autres modes de réalisation, les procédés selon l'invention consistent à employer au moins deux algorithmes et au moins deux valeurs de qualité pour l'appel d'allèle. L'invention concerne également des algorithmes individuels uniques destinés à l'appel d'allèle.
PCT/US2001/023629 2000-07-21 2001-07-23 Procedes, systemes et articles manufactures destines a evaluer des donnees biologiques Ceased WO2002008469A2 (fr)

Priority Applications (4)

Application Number Priority Date Filing Date Title
JP2002513951A JP2004516455A (ja) 2000-07-21 2001-07-23 生物学的データを評価するための方法、システム、および製品
AU2002211212A AU2002211212A1 (en) 2000-07-21 2001-07-23 Methods, systems, and articles of manufacture for evaluating biological data
EP01979226A EP1349960A2 (fr) 2000-07-21 2001-07-23 Procedes, systemes et articles manufactures destines a evaluer des donnees biologiques
CA002416764A CA2416764A1 (fr) 2000-07-21 2001-07-23 Procedes, systemes et articles manufactures destines a evaluer des donnees biologiques

Applications Claiming Priority (8)

Application Number Priority Date Filing Date Title
US21969700P 2000-07-21 2000-07-21
US60/219,697 2000-07-21
US22755600P 2000-08-23 2000-08-23
US60/227,556 2000-08-23
US72491000A 2000-11-28 2000-11-28
US09/724,910 2000-11-28
US29012901P 2001-05-10 2001-05-10
US60/290,129 2001-05-10

Publications (3)

Publication Number Publication Date
WO2002008469A2 WO2002008469A2 (fr) 2002-01-31
WO2002008469A3 WO2002008469A3 (fr) 2003-07-17
WO2002008469A9 true WO2002008469A9 (fr) 2003-11-20

Family

ID=27499158

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2001/023629 Ceased WO2002008469A2 (fr) 2000-07-21 2001-07-23 Procedes, systemes et articles manufactures destines a evaluer des donnees biologiques

Country Status (5)

Country Link
EP (1) EP1349960A2 (fr)
JP (1) JP2004516455A (fr)
AU (1) AU2002211212A1 (fr)
CA (1) CA2416764A1 (fr)
WO (1) WO2002008469A2 (fr)

Families Citing this family (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP2005531853A (ja) * 2002-06-28 2005-10-20 アプレラ コーポレイション Ｓｎｐ遺伝子型クラスタリングのためのシステムおよび方法
JP4713138B2 (ja) * 2004-12-06 2011-06-29 株式会社日立ソリューションズ 遺伝子情報の表示方法及び表示装置及びプログラム
EP1862929A1 (fr) * 2006-02-28 2007-12-05 Hitachi Software Engineering Co., Ltd. Procédé et dispositif d'évaluation de résultat de genotypage
US20090277790A1 (en) 2006-04-14 2009-11-12 Nec Corporation Individual identification method and apparatus
CN105579676B (zh) * 2013-08-27 2017-11-14 日产自动车株式会社 内燃机的多连杆式活塞曲柄机构
JP2017532699A (ja) * 2014-09-05 2017-11-02 ナントミクス，エルエルシー 起源の判定のためのシステムと方法
AU2015318017B2 (en) * 2014-09-18 2022-02-03 Illumina, Inc. Methods and systems for analyzing nucleic acid sequencing data

Family Cites Families (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5580728A (en) * 1994-06-17 1996-12-03 Perlin; Mark W. Method and system for genotyping
US6019896A (en) * 1998-03-06 2000-02-01 Molecular Dynamics, Inc. Method for using a quality metric to assess the quality of biochemical separations
CA2328881A1 (fr) * 1998-04-16 1999-10-21 Northeastern University Systeme expert d'analyse des electrophoregrammes d'adn

Also Published As

Publication number Publication date
JP2004516455A (ja) 2004-06-03
WO2002008469A3 (fr) 2003-07-17
EP1349960A2 (fr) 2003-10-08
CA2416764A1 (fr) 2002-01-31
WO2002008469A2 (fr) 2002-01-31
AU2002211212A1 (en) 2002-02-05

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